2fid: Difference between revisions

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-{{Seed}}
-[[Image:2fid.png|left|200px]]
-<!--
+==Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin==
-The line below this paragraph, containing "STRUCTURE_2fid", creates the "Structure Box" on the page.
+<StructureSection load='2fid' size='340' side='right'caption='[[2fid]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2fid]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FID FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2fid|  PDB=2fid  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fid OCA], [https://pdbe.org/2fid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fid RCSB], [https://www.ebi.ac.uk/pdbsum/2fid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fid ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UBC_BOVIN UBC_BOVIN] Ubiquitin: Exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity).
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fi/2fid_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2fid ConSurf].
+<div style="clear:both"></div>
-===Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin===
+==See Also==
+*[[Rab5 GDP/GTP exchange factor|Rab5 GDP/GTP exchange factor]]
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
-<!--
+__TOC__
-The line below this paragraph, {{ABSTRACT_PUBMED_16462746}}, adds the Publication Abstract to the page
+</StructureSection>
-(as it appears on PubMed at http://www.pubmed.gov), where 16462746 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_16462746}}
-==About this Structure==
-FID is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FID OCA].
-==Reference==
-Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5., Lee S, Tsai YC, Mattera R, Smith WJ, Kostelansky MS, Weissman AM, Bonifacino JS, Hurley JH, Nat Struct Mol Biol. 2006 Mar;13(3):264-71. Epub 2006 Feb 5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16462746 16462746]
 [[Category: Bos taurus]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Hurley, J H.]]
+[[Category: Hurley JH]]
-[[Category: Lee, S.]]
+[[Category: Lee S]]
-[[Category: Helix]]
-[[Category: Zinc finger]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 14:10:09 2008''